The present disclosure provides methods for manufacturing a shelf-stable food product. In a general embodiment, the methods include acoustically mixing the food product with an acoustic mixing device during thermal processing of the food product. The methods of the present disclosure provide several advantages including, but not limited to, rapid achievement of a uniform temperature distribution during thermal processing, retention of nutrient content and organoleptic properties of the food product, and retention of particle integrity in the food product during and after mixing.